Fluorine in PDB 2gh6: Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Protein crystallography data
The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6
was solved by
T.K.Nielsen,
C.Hildmann,
D.Riester,
D.Wegener,
A.Schwienhorst,
R.Ficner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.84 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.507,
94.897,
123.301,
90.00,
104.28,
90.00
|
R / Rfree (%)
|
15.8 /
21.4
|
Other elements in 2gh6:
The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound also contains other interesting chemical elements:
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Fluorine atom in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
(pdb code 2gh6). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the
Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 1 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F9452
b:24.6
occ:1.00
|
F3
|
A:CF39452
|
0.0
|
24.6
|
1.0
|
C15
|
A:CF39452
|
1.3
|
23.1
|
1.0
|
F2
|
A:CF39452
|
2.2
|
26.0
|
1.0
|
F1
|
A:CF39452
|
2.2
|
26.7
|
1.0
|
C13
|
A:CF39452
|
2.3
|
23.5
|
0.5
|
C13
|
A:CF39452
|
2.4
|
24.0
|
0.5
|
C11
|
A:CF39452
|
2.9
|
25.6
|
0.5
|
O2
|
A:CF39452
|
2.9
|
14.5
|
0.5
|
SG
|
A:CYS153
|
3.1
|
19.8
|
1.0
|
CD2
|
A:HIS143
|
3.2
|
17.0
|
1.0
|
CD2
|
A:HIS142
|
3.2
|
15.8
|
1.0
|
O
|
A:GLY151
|
3.3
|
20.4
|
1.0
|
C11
|
A:CF39452
|
3.3
|
25.3
|
0.5
|
NE2
|
A:HIS142
|
3.4
|
15.6
|
1.0
|
O2
|
A:CF39452
|
3.5
|
17.8
|
0.5
|
NE2
|
A:HIS143
|
3.8
|
17.1
|
1.0
|
CG
|
A:PRO140
|
3.8
|
15.0
|
1.0
|
CB
|
A:PRO140
|
3.9
|
14.9
|
1.0
|
CG
|
A:HIS143
|
4.0
|
16.8
|
1.0
|
C9
|
A:CF39452
|
4.3
|
27.9
|
1.0
|
C
|
A:GLY151
|
4.5
|
21.1
|
1.0
|
CG
|
A:HIS142
|
4.6
|
17.3
|
1.0
|
OE2
|
A:GLU309
|
4.6
|
18.6
|
1.0
|
CB
|
A:HIS143
|
4.6
|
17.3
|
1.0
|
ZN
|
A:ZN9451
|
4.6
|
31.0
|
0.5
|
CE1
|
A:HIS142
|
4.7
|
16.3
|
1.0
|
N
|
A:HIS143
|
4.7
|
16.7
|
1.0
|
OD2
|
A:ASP180
|
4.7
|
15.4
|
1.0
|
OH
|
A:TYR312
|
4.8
|
21.4
|
1.0
|
N
|
A:HIS142
|
4.8
|
16.4
|
1.0
|
CE1
|
A:HIS143
|
4.8
|
17.0
|
1.0
|
CB
|
A:CYS153
|
4.8
|
18.9
|
1.0
|
ND1
|
A:HIS143
|
4.9
|
16.5
|
1.0
|
N
|
A:GLY141
|
5.0
|
16.2
|
1.0
|
CB
|
A:PHE152
|
5.0
|
20.6
|
1.0
|
|
Fluorine binding site 2 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 2 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F9452
b:26.7
occ:1.00
|
F1
|
A:CF39452
|
0.0
|
26.7
|
1.0
|
C15
|
A:CF39452
|
1.3
|
23.1
|
1.0
|
F2
|
A:CF39452
|
2.1
|
26.0
|
1.0
|
F3
|
A:CF39452
|
2.2
|
24.6
|
1.0
|
C13
|
A:CF39452
|
2.2
|
24.0
|
0.5
|
C13
|
A:CF39452
|
2.5
|
23.5
|
0.5
|
CG
|
A:PRO140
|
2.9
|
15.0
|
1.0
|
O2
|
A:CF39452
|
3.0
|
17.8
|
0.5
|
C11
|
A:CF39452
|
3.0
|
25.3
|
0.5
|
C11
|
A:CF39452
|
3.0
|
25.6
|
0.5
|
OH
|
A:TYR312
|
3.0
|
21.4
|
1.0
|
O
|
A:HOH9535
|
3.1
|
21.7
|
1.0
|
CB
|
A:PRO140
|
3.4
|
14.9
|
1.0
|
O2
|
A:CF39452
|
3.6
|
14.5
|
0.5
|
CD1
|
A:PHE152
|
3.9
|
19.4
|
1.0
|
CA
|
A:GLY310
|
4.0
|
17.3
|
1.0
|
O
|
A:GLY151
|
4.0
|
20.4
|
1.0
|
N
|
A:GLY310
|
4.2
|
16.9
|
1.0
|
CB
|
A:PHE152
|
4.3
|
20.6
|
1.0
|
CD
|
A:PRO140
|
4.3
|
16.0
|
1.0
|
CZ
|
A:TYR312
|
4.3
|
17.3
|
1.0
|
C9
|
A:CF39452
|
4.4
|
27.9
|
1.0
|
SG
|
A:CYS153
|
4.5
|
19.8
|
1.0
|
ZN
|
A:ZN9451
|
4.5
|
31.0
|
0.5
|
CG
|
A:PHE152
|
4.5
|
20.7
|
1.0
|
C
|
A:GLU309
|
4.6
|
16.1
|
1.0
|
OD2
|
A:ASP180
|
4.7
|
15.4
|
1.0
|
O
|
A:GLU309
|
4.8
|
17.4
|
1.0
|
CE1
|
A:PHE152
|
4.8
|
20.9
|
1.0
|
CA
|
A:PRO140
|
4.8
|
16.2
|
1.0
|
NE2
|
A:HIS142
|
4.8
|
15.6
|
1.0
|
CD2
|
A:HIS142
|
4.9
|
15.8
|
1.0
|
CD2
|
A:HIS143
|
5.0
|
17.0
|
1.0
|
|
Fluorine binding site 3 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 3 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F9452
b:26.0
occ:1.00
|
F2
|
A:CF39452
|
0.0
|
26.0
|
1.0
|
C15
|
A:CF39452
|
1.3
|
23.1
|
1.0
|
F1
|
A:CF39452
|
2.1
|
26.7
|
1.0
|
F3
|
A:CF39452
|
2.2
|
24.6
|
1.0
|
C13
|
A:CF39452
|
2.4
|
24.0
|
0.5
|
C13
|
A:CF39452
|
2.4
|
23.5
|
0.5
|
O2
|
A:CF39452
|
2.7
|
17.8
|
0.5
|
O2
|
A:CF39452
|
2.8
|
14.5
|
0.5
|
OD2
|
A:ASP180
|
2.9
|
15.4
|
1.0
|
N
|
A:GLY310
|
3.0
|
16.9
|
1.0
|
NE2
|
A:HIS142
|
3.1
|
15.6
|
1.0
|
CD2
|
A:HIS142
|
3.3
|
15.8
|
1.0
|
CA
|
A:GLY310
|
3.4
|
17.3
|
1.0
|
ZN
|
A:ZN9451
|
3.6
|
31.0
|
0.5
|
C
|
A:GLU309
|
3.6
|
16.1
|
1.0
|
CB
|
A:PRO140
|
3.7
|
14.9
|
1.0
|
C11
|
A:CF39452
|
3.7
|
25.3
|
0.5
|
C11
|
A:CF39452
|
3.8
|
25.6
|
0.5
|
CB
|
A:GLU309
|
3.8
|
15.5
|
1.0
|
CG
|
A:ASP180
|
3.8
|
17.4
|
1.0
|
OE2
|
A:GLU309
|
4.0
|
18.6
|
1.0
|
CG
|
A:PRO140
|
4.0
|
15.0
|
1.0
|
CA
|
A:GLU309
|
4.1
|
16.6
|
1.0
|
OH
|
A:TYR312
|
4.2
|
21.4
|
1.0
|
O
|
A:GLU309
|
4.3
|
17.4
|
1.0
|
CE1
|
A:HIS142
|
4.3
|
16.3
|
1.0
|
OD1
|
A:ASP180
|
4.4
|
16.0
|
1.0
|
O
|
A:HOH9535
|
4.4
|
21.7
|
1.0
|
CG
|
A:HIS142
|
4.6
|
17.3
|
1.0
|
CD2
|
A:HIS143
|
4.8
|
17.0
|
1.0
|
CD
|
A:GLU309
|
4.8
|
18.2
|
1.0
|
SG
|
A:CYS153
|
4.8
|
19.8
|
1.0
|
CB
|
A:ASP180
|
4.9
|
15.7
|
1.0
|
CG
|
A:GLU309
|
4.9
|
16.4
|
1.0
|
OD2
|
A:ASP268
|
4.9
|
17.1
|
1.0
|
NE2
|
A:HIS143
|
4.9
|
17.1
|
1.0
|
C
|
A:GLY310
|
4.9
|
17.9
|
1.0
|
C9
|
A:CF39452
|
5.0
|
27.9
|
1.0
|
|
Fluorine binding site 4 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 4 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F9552
b:20.6
occ:1.00
|
F3
|
B:CF39552
|
0.0
|
20.6
|
1.0
|
C15
|
B:CF39552
|
1.3
|
18.2
|
1.0
|
F2
|
B:CF39552
|
2.2
|
18.9
|
1.0
|
F1
|
B:CF39552
|
2.2
|
19.7
|
1.0
|
C13
|
B:CF39552
|
2.3
|
17.9
|
0.5
|
C13
|
B:CF39552
|
2.4
|
17.4
|
0.5
|
C11
|
B:CF39552
|
2.8
|
19.2
|
0.5
|
O2
|
B:CF39552
|
2.9
|
6.9
|
0.5
|
CD2
|
B:HIS143
|
3.2
|
16.1
|
1.0
|
SG
|
B:CYS153
|
3.2
|
16.6
|
1.0
|
CD2
|
B:HIS142
|
3.2
|
15.5
|
1.0
|
O
|
B:GLY151
|
3.3
|
21.9
|
1.0
|
NE2
|
B:HIS142
|
3.3
|
16.3
|
1.0
|
C11
|
B:CF39552
|
3.4
|
20.1
|
0.5
|
O2
|
B:CF39552
|
3.5
|
5.5
|
0.5
|
NE2
|
B:HIS143
|
3.6
|
19.4
|
1.0
|
CB
|
B:PRO140
|
3.8
|
15.1
|
1.0
|
CG
|
B:PRO140
|
3.8
|
14.5
|
1.0
|
CG
|
B:HIS143
|
4.1
|
18.3
|
1.0
|
C9
|
B:CF39552
|
4.3
|
23.2
|
1.0
|
C
|
B:GLY151
|
4.5
|
21.5
|
1.0
|
CG
|
B:HIS142
|
4.6
|
15.1
|
1.0
|
OE2
|
B:GLU309
|
4.6
|
18.9
|
1.0
|
CE1
|
B:HIS142
|
4.6
|
13.6
|
1.0
|
CE1
|
B:HIS143
|
4.7
|
16.9
|
1.0
|
ZN
|
B:ZN9551
|
4.7
|
26.9
|
0.5
|
OH
|
B:TYR312
|
4.8
|
18.8
|
1.0
|
N
|
B:HIS143
|
4.8
|
17.0
|
1.0
|
OD2
|
B:ASP180
|
4.8
|
17.3
|
1.0
|
N
|
B:HIS142
|
4.8
|
15.8
|
1.0
|
CB
|
B:HIS143
|
4.9
|
18.4
|
1.0
|
N
|
B:GLY141
|
4.9
|
15.2
|
1.0
|
CB
|
B:CYS153
|
4.9
|
18.2
|
1.0
|
ND1
|
B:HIS143
|
4.9
|
19.4
|
1.0
|
|
Fluorine binding site 5 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 5 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F9552
b:19.7
occ:1.00
|
F1
|
B:CF39552
|
0.0
|
19.7
|
1.0
|
C15
|
B:CF39552
|
1.3
|
18.2
|
1.0
|
F2
|
B:CF39552
|
2.1
|
18.9
|
1.0
|
F3
|
B:CF39552
|
2.2
|
20.6
|
1.0
|
C13
|
B:CF39552
|
2.2
|
17.4
|
0.5
|
C13
|
B:CF39552
|
2.5
|
17.9
|
0.5
|
O2
|
B:CF39552
|
2.9
|
5.5
|
0.5
|
C11
|
B:CF39552
|
2.9
|
20.1
|
0.5
|
OH
|
B:TYR312
|
2.9
|
18.8
|
1.0
|
O
|
B:HOH9570
|
3.0
|
14.8
|
1.0
|
C11
|
B:CF39552
|
3.1
|
19.2
|
0.5
|
CG
|
B:PRO140
|
3.1
|
14.5
|
1.0
|
CB
|
B:PRO140
|
3.4
|
15.1
|
1.0
|
O2
|
B:CF39552
|
3.6
|
6.9
|
0.5
|
CD1
|
B:PHE152
|
3.9
|
20.6
|
1.0
|
O
|
B:GLY151
|
3.9
|
21.9
|
1.0
|
CA
|
B:GLY310
|
3.9
|
15.7
|
1.0
|
N
|
B:GLY310
|
4.2
|
16.0
|
1.0
|
CZ
|
B:TYR312
|
4.2
|
22.2
|
1.0
|
CB
|
B:PHE152
|
4.3
|
20.4
|
1.0
|
C9
|
B:CF39552
|
4.3
|
23.2
|
1.0
|
CD
|
B:PRO140
|
4.4
|
16.1
|
1.0
|
CG
|
B:PHE152
|
4.5
|
21.4
|
1.0
|
ZN
|
B:ZN9551
|
4.5
|
26.9
|
0.5
|
SG
|
B:CYS153
|
4.7
|
16.6
|
1.0
|
C
|
B:GLU309
|
4.7
|
16.0
|
1.0
|
OD2
|
B:ASP180
|
4.7
|
17.3
|
1.0
|
CE1
|
B:PHE152
|
4.8
|
21.7
|
1.0
|
NE2
|
B:HIS142
|
4.9
|
16.3
|
1.0
|
CA
|
B:PRO140
|
4.9
|
15.6
|
1.0
|
CD2
|
B:HIS143
|
4.9
|
16.1
|
1.0
|
O
|
B:GLU309
|
5.0
|
16.4
|
1.0
|
|
Fluorine binding site 6 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 6 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F9552
b:18.9
occ:1.00
|
F2
|
B:CF39552
|
0.0
|
18.9
|
1.0
|
C15
|
B:CF39552
|
1.3
|
18.2
|
1.0
|
F1
|
B:CF39552
|
2.1
|
19.7
|
1.0
|
F3
|
B:CF39552
|
2.2
|
20.6
|
1.0
|
C13
|
B:CF39552
|
2.4
|
17.4
|
0.5
|
C13
|
B:CF39552
|
2.4
|
17.9
|
0.5
|
O2
|
B:CF39552
|
2.7
|
5.5
|
0.5
|
O2
|
B:CF39552
|
2.9
|
6.9
|
0.5
|
OD2
|
B:ASP180
|
2.9
|
17.3
|
1.0
|
N
|
B:GLY310
|
2.9
|
16.0
|
1.0
|
NE2
|
B:HIS142
|
3.2
|
16.3
|
1.0
|
CA
|
B:GLY310
|
3.3
|
15.7
|
1.0
|
CD2
|
B:HIS142
|
3.5
|
15.5
|
1.0
|
C
|
B:GLU309
|
3.6
|
16.0
|
1.0
|
ZN
|
B:ZN9551
|
3.6
|
26.9
|
0.5
|
C11
|
B:CF39552
|
3.7
|
20.1
|
0.5
|
C11
|
B:CF39552
|
3.7
|
19.2
|
0.5
|
CB
|
B:PRO140
|
3.7
|
15.1
|
1.0
|
CG
|
B:ASP180
|
3.8
|
16.1
|
1.0
|
CB
|
B:GLU309
|
3.8
|
16.5
|
1.0
|
CA
|
B:GLU309
|
4.0
|
16.2
|
1.0
|
OE2
|
B:GLU309
|
4.1
|
18.9
|
1.0
|
OD1
|
B:ASP180
|
4.2
|
14.6
|
1.0
|
CG
|
B:PRO140
|
4.2
|
14.5
|
1.0
|
OH
|
B:TYR312
|
4.2
|
18.8
|
1.0
|
O
|
B:GLU309
|
4.4
|
16.4
|
1.0
|
CE1
|
B:HIS142
|
4.4
|
13.6
|
1.0
|
O
|
B:HOH9570
|
4.4
|
14.8
|
1.0
|
CG
|
B:HIS142
|
4.7
|
15.1
|
1.0
|
C
|
B:GLY310
|
4.7
|
16.2
|
1.0
|
NE2
|
B:HIS143
|
4.8
|
19.4
|
1.0
|
CB
|
B:ASP180
|
4.8
|
15.3
|
1.0
|
CG
|
B:GLU309
|
4.9
|
16.4
|
1.0
|
OD2
|
B:ASP268
|
4.9
|
17.1
|
1.0
|
CD2
|
B:HIS143
|
4.9
|
16.1
|
1.0
|
CD
|
B:GLU309
|
4.9
|
17.9
|
1.0
|
C9
|
B:CF39552
|
4.9
|
23.2
|
1.0
|
SG
|
B:CYS153
|
5.0
|
16.6
|
1.0
|
|
Fluorine binding site 7 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 7 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F9652
b:23.8
occ:1.00
|
F3
|
C:CF39652
|
0.0
|
23.8
|
1.0
|
C15
|
C:CF39652
|
1.3
|
22.0
|
1.0
|
F2
|
C:CF39652
|
2.1
|
24.9
|
1.0
|
F1
|
C:CF39652
|
2.2
|
23.6
|
1.0
|
C13
|
C:CF39652
|
2.2
|
22.1
|
0.5
|
C13
|
C:CF39652
|
2.5
|
23.6
|
0.5
|
O2
|
C:CF39652
|
2.9
|
12.0
|
0.5
|
C11
|
C:CF39652
|
3.0
|
25.1
|
0.5
|
SG
|
C:CYS153
|
3.1
|
18.6
|
1.0
|
CD2
|
C:HIS143
|
3.2
|
10.7
|
1.0
|
C11
|
C:CF39652
|
3.2
|
23.6
|
0.5
|
CD2
|
C:HIS142
|
3.2
|
13.4
|
1.0
|
NE2
|
C:HIS142
|
3.4
|
15.1
|
1.0
|
O
|
C:GLY151
|
3.4
|
23.2
|
1.0
|
O2
|
C:CF39652
|
3.6
|
16.3
|
0.5
|
CG
|
C:PRO140
|
3.7
|
17.1
|
1.0
|
CB
|
C:PRO140
|
3.7
|
17.1
|
1.0
|
NE2
|
C:HIS143
|
3.7
|
14.9
|
1.0
|
CG
|
C:HIS143
|
4.1
|
15.7
|
1.0
|
OE2
|
C:GLU309
|
4.4
|
19.0
|
1.0
|
C9
|
C:CF39652
|
4.5
|
27.5
|
1.0
|
ZN
|
C:ZN9651
|
4.5
|
31.3
|
0.5
|
CG
|
C:HIS142
|
4.6
|
16.2
|
1.0
|
C
|
C:GLY151
|
4.7
|
22.9
|
1.0
|
CE1
|
C:HIS142
|
4.7
|
16.2
|
1.0
|
N
|
C:HIS143
|
4.7
|
17.5
|
1.0
|
CE1
|
C:HIS143
|
4.8
|
16.0
|
1.0
|
N
|
C:HIS142
|
4.8
|
16.4
|
1.0
|
CB
|
C:HIS143
|
4.8
|
17.8
|
1.0
|
OD2
|
C:ASP180
|
4.8
|
18.6
|
1.0
|
OH
|
C:TYR312
|
4.8
|
20.4
|
1.0
|
CB
|
C:CYS153
|
4.9
|
19.4
|
1.0
|
N
|
C:GLY141
|
4.9
|
15.8
|
1.0
|
CA
|
C:PRO140
|
5.0
|
17.2
|
1.0
|
ND1
|
C:HIS143
|
5.0
|
17.6
|
1.0
|
C
|
C:PRO140
|
5.0
|
17.0
|
1.0
|
CB
|
C:PHE152
|
5.0
|
22.2
|
1.0
|
O
|
C:HOH9677
|
5.0
|
20.1
|
1.0
|
|
Fluorine binding site 8 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 8 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F9652
b:23.6
occ:1.00
|
F1
|
C:CF39652
|
0.0
|
23.6
|
1.0
|
C15
|
C:CF39652
|
1.3
|
22.0
|
1.0
|
F2
|
C:CF39652
|
2.1
|
24.9
|
1.0
|
F3
|
C:CF39652
|
2.2
|
23.8
|
1.0
|
C13
|
C:CF39652
|
2.2
|
23.6
|
0.5
|
C13
|
C:CF39652
|
2.4
|
22.1
|
0.5
|
C11
|
C:CF39652
|
2.9
|
23.6
|
0.5
|
O
|
C:HOH9677
|
2.9
|
20.1
|
1.0
|
O2
|
C:CF39652
|
2.9
|
16.3
|
0.5
|
OH
|
C:TYR312
|
3.0
|
20.4
|
1.0
|
CG
|
C:PRO140
|
3.1
|
17.1
|
1.0
|
C11
|
C:CF39652
|
3.1
|
25.1
|
0.5
|
CB
|
C:PRO140
|
3.4
|
17.1
|
1.0
|
O2
|
C:CF39652
|
3.5
|
12.0
|
0.5
|
CA
|
C:GLY310
|
3.9
|
17.5
|
1.0
|
CD1
|
C:PHE152
|
4.0
|
21.9
|
1.0
|
O
|
C:GLY151
|
4.1
|
23.2
|
1.0
|
N
|
C:GLY310
|
4.2
|
17.4
|
1.0
|
CB
|
C:PHE152
|
4.3
|
22.2
|
1.0
|
CZ
|
C:TYR312
|
4.3
|
18.7
|
1.0
|
C9
|
C:CF39652
|
4.4
|
27.5
|
1.0
|
ZN
|
C:ZN9651
|
4.4
|
31.3
|
0.5
|
CD
|
C:PRO140
|
4.4
|
18.3
|
1.0
|
C
|
C:GLU309
|
4.6
|
18.1
|
1.0
|
SG
|
C:CYS153
|
4.6
|
18.6
|
1.0
|
CG
|
C:PHE152
|
4.6
|
21.7
|
1.0
|
OD2
|
C:ASP180
|
4.8
|
18.6
|
1.0
|
O
|
C:GLU309
|
4.9
|
18.9
|
1.0
|
CA
|
C:PRO140
|
4.9
|
17.2
|
1.0
|
CD2
|
C:HIS143
|
4.9
|
10.7
|
1.0
|
NE2
|
C:HIS142
|
4.9
|
15.1
|
1.0
|
CE1
|
C:PHE152
|
5.0
|
22.1
|
1.0
|
|
Fluorine binding site 9 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 9 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F9652
b:24.9
occ:1.00
|
F2
|
C:CF39652
|
0.0
|
24.9
|
1.0
|
C15
|
C:CF39652
|
1.3
|
22.0
|
1.0
|
F1
|
C:CF39652
|
2.1
|
23.6
|
1.0
|
F3
|
C:CF39652
|
2.1
|
23.8
|
1.0
|
C13
|
C:CF39652
|
2.3
|
23.6
|
0.5
|
C13
|
C:CF39652
|
2.4
|
22.1
|
0.5
|
O2
|
C:CF39652
|
2.7
|
16.3
|
0.5
|
O2
|
C:CF39652
|
2.8
|
12.0
|
0.5
|
N
|
C:GLY310
|
2.9
|
17.4
|
1.0
|
OD2
|
C:ASP180
|
2.9
|
18.6
|
1.0
|
CA
|
C:GLY310
|
3.2
|
17.5
|
1.0
|
NE2
|
C:HIS142
|
3.3
|
15.1
|
1.0
|
ZN
|
C:ZN9651
|
3.3
|
31.3
|
0.5
|
CD2
|
C:HIS142
|
3.5
|
13.4
|
1.0
|
C
|
C:GLU309
|
3.6
|
18.1
|
1.0
|
C11
|
C:CF39652
|
3.7
|
23.6
|
0.5
|
C11
|
C:CF39652
|
3.7
|
25.1
|
0.5
|
CB
|
C:PRO140
|
3.8
|
17.1
|
1.0
|
CG
|
C:ASP180
|
3.8
|
18.4
|
1.0
|
CB
|
C:GLU309
|
3.8
|
17.3
|
1.0
|
CA
|
C:GLU309
|
4.0
|
17.9
|
1.0
|
OE2
|
C:GLU309
|
4.1
|
19.0
|
1.0
|
OH
|
C:TYR312
|
4.1
|
20.4
|
1.0
|
OD1
|
C:ASP180
|
4.2
|
17.9
|
1.0
|
CG
|
C:PRO140
|
4.2
|
17.1
|
1.0
|
O
|
C:HOH9677
|
4.2
|
20.1
|
1.0
|
O
|
C:GLU309
|
4.3
|
18.9
|
1.0
|
CE1
|
C:HIS142
|
4.4
|
16.2
|
1.0
|
OD2
|
C:ASP268
|
4.7
|
16.2
|
1.0
|
C
|
C:GLY310
|
4.7
|
17.8
|
1.0
|
CG
|
C:HIS142
|
4.8
|
16.2
|
1.0
|
NE2
|
C:HIS143
|
4.8
|
14.9
|
1.0
|
CD2
|
C:HIS143
|
4.8
|
10.7
|
1.0
|
CG
|
C:GLU309
|
4.9
|
18.4
|
1.0
|
CB
|
C:ASP180
|
4.9
|
17.1
|
1.0
|
CD
|
C:GLU309
|
4.9
|
19.6
|
1.0
|
C9
|
C:CF39652
|
5.0
|
27.5
|
1.0
|
SG
|
C:CYS153
|
5.0
|
18.6
|
1.0
|
|
Fluorine binding site 10 out
of 12 in 2gh6
Go back to
Fluorine Binding Sites List in 2gh6
Fluorine binding site 10 out
of 12 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F9752
b:24.8
occ:1.00
|
F3
|
D:CF39752
|
0.0
|
24.8
|
1.0
|
C15
|
D:CF39752
|
1.3
|
23.7
|
1.0
|
F1
|
D:CF39752
|
2.2
|
23.3
|
1.0
|
F2
|
D:CF39752
|
2.2
|
24.9
|
1.0
|
C13
|
D:CF39752
|
2.2
|
23.3
|
0.5
|
C13
|
D:CF39752
|
2.4
|
23.0
|
0.5
|
C11
|
D:CF39752
|
2.9
|
25.9
|
0.5
|
O2
|
D:CF39752
|
3.0
|
16.3
|
0.5
|
C11
|
D:CF39752
|
3.1
|
26.0
|
0.5
|
SG
|
D:CYS153
|
3.1
|
21.2
|
1.0
|
CD2
|
D:HIS143
|
3.2
|
15.5
|
1.0
|
O
|
D:GLY151
|
3.2
|
22.6
|
1.0
|
CD2
|
D:HIS142
|
3.3
|
16.9
|
1.0
|
NE2
|
D:HIS142
|
3.4
|
21.1
|
1.0
|
O2
|
D:CF39752
|
3.5
|
15.4
|
0.5
|
CG
|
D:PRO140
|
3.7
|
17.3
|
1.0
|
NE2
|
D:HIS143
|
3.7
|
17.7
|
1.0
|
CB
|
D:PRO140
|
3.8
|
17.5
|
1.0
|
CG
|
D:HIS143
|
4.1
|
18.8
|
1.0
|
C9
|
D:CF39752
|
4.4
|
28.4
|
1.0
|
C
|
D:GLY151
|
4.4
|
23.4
|
1.0
|
OE2
|
D:GLU309
|
4.6
|
17.4
|
1.0
|
CG
|
D:HIS142
|
4.7
|
19.4
|
1.0
|
ZN
|
D:ZN9751
|
4.7
|
29.7
|
0.5
|
N
|
D:HIS142
|
4.7
|
18.3
|
1.0
|
OH
|
D:TYR312
|
4.7
|
20.4
|
1.0
|
CB
|
D:HIS143
|
4.7
|
20.0
|
1.0
|
CE1
|
D:HIS142
|
4.8
|
18.1
|
1.0
|
CE1
|
D:HIS143
|
4.8
|
16.3
|
1.0
|
N
|
D:GLY141
|
4.8
|
17.5
|
1.0
|
N
|
D:HIS143
|
4.8
|
19.8
|
1.0
|
CB
|
D:CYS153
|
4.9
|
21.9
|
1.0
|
CD1
|
D:PHE152
|
5.0
|
24.2
|
1.0
|
ND1
|
D:HIS143
|
5.0
|
17.8
|
1.0
|
OD2
|
D:ASP180
|
5.0
|
21.7
|
1.0
|
CB
|
D:PHE152
|
5.0
|
22.8
|
1.0
|
|
Reference:
T.K.Nielsen,
C.Hildmann,
D.Riester,
D.Wegener,
A.Schwienhorst,
R.Ficner.
Complex Structure of A Bacterial Class 2 Histone Deacetylase Homologue with A Trifluoromethylketone Inhibitor. Acta Crystallogr.,Sect.F V. 63 270 2007.
ISSN: ESSN 1744-3091
PubMed: 17401192
DOI: 10.1107/S1744309107012377
Page generated: Wed Jul 31 14:35:13 2024
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